Contacts of the helix formed by residues 98 - 116 (chain A) in PDB entry 4MT7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE 3.6 0.4 + - - -
97A GLY* 1.3 69.0 - - - -
99A ILE* 1.3 58.0 + - - +
100A GLU 3.2 3.4 - - - +
101A ASP* 3.0 19.1 + - + +
102A ILE* 2.9 27.7 + - - +
140A ILE* 2.7 36.7 + - - +
143A GLU* 2.6 41.5 + - - +
144A TYR* 3.4 28.4 - - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.7 26.7 - - + -
72A ILE* 4.0 24.7 - - + -
73A CYS* 4.0 12.6 - - - -
77A LEU* 4.5 7.9 - - + -
96A PHE* 3.3 41.0 + - + +
97A GLY 3.2 2.7 - - - +
98A ASN* 1.3 78.1 + - - +
100A GLU* 1.3 60.0 + - - +
102A ILE* 3.3 11.7 + - + +
103A TYR* 2.9 27.5 + - - +
144A TYR* 3.7 23.1 - - + +
186A LEU* 5.5 1.3 - - + -
189A PRO* 3.7 15.5 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A CYS* 3.7 23.4 - - + +
77A LEU* 4.0 11.4 - - + +
81A ARG* 2.7 44.1 + - - -
97A GLY 4.8 1.3 + - - +
98A ASN 3.2 0.8 - - - -
99A ILE* 1.3 77.3 - - - +
101A ASP* 1.3 61.1 + - - +
103A TYR* 3.3 4.7 + - + +
104A ARG* 2.9 71.8 + - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASN* 3.0 25.1 + - + +
100A GLU* 1.3 79.1 - - - +
102A ILE* 1.3 60.7 + - - +
104A ARG* 3.1 22.9 + - - +
105A PHE* 2.9 23.4 + - - +
140A ILE* 3.9 14.9 - - + +
143A GLU* 5.7 0.3 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.9 13.5 - - - +
69A LEU* 3.7 23.6 - - + -
98A ASN* 2.9 14.5 + - - +
99A ILE* 3.4 15.5 - - + +
101A ASP* 1.3 75.0 - - - +
103A TYR* 1.3 57.8 + - - +
105A PHE* 3.1 5.0 + - - +
106A GLN* 2.9 27.3 + - - +
140A ILE* 3.5 28.4 - - + +
141A TYR* 3.9 18.4 - - + +
144A TYR* 3.5 44.0 - - + -
189A PRO* 4.4 8.7 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.9 24.2 - - + -
69A LEU* 3.7 25.6 - - + -
70A LYS* 3.4 39.6 - - + +
73A CYS* 3.9 27.4 - - + -
74A GLU* 6.4 0.4 - - + -
99A ILE 2.9 14.4 + - - +
100A GLU* 3.5 9.9 - - + +
102A ILE* 1.3 75.8 - - - +
104A ARG* 1.3 67.7 + - - +
106A GLN* 3.2 0.9 + - - +
107A MET* 2.9 52.0 + - + +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 2.9 62.3 + - - +
101A ASP* 3.1 24.2 + - - +
103A TYR* 1.3 81.2 - - - +
105A PHE* 1.3 61.1 + - - +
107A MET* 3.8 32.9 - - + +
108A GLY* 3.8 4.3 + - - -
111A ARG* 5.5 0.7 + - - -
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP 2.9 11.9 + - - +
102A ILE 3.5 7.4 - - - +
104A ARG* 1.3 75.2 - - - +
106A GLN* 1.3 78.0 + - - +
107A MET 3.2 0.2 - - - -
108A GLY* 3.2 4.3 + - - -
109A PHE* 3.0 31.1 + - + +
134A HIS* 4.0 23.1 - + + -
137A GLY* 3.5 26.0 - - - -
138A PHE* 3.5 52.7 - + - -
140A ILE* 3.8 19.5 - - + -
141A TYR* 4.5 6.7 - + - -
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 2.9 28.3 + - - -
65A TYR* 3.3 35.8 - - + -
66A ILE* 4.0 15.0 - - + -
69A LEU* 3.8 11.4 - - + -
102A ILE 2.9 15.4 + - - +
103A TYR 3.6 4.0 - - - +
105A PHE* 1.3 91.6 - - - +
107A MET* 1.3 60.5 + - - +
109A PHE* 4.2 9.1 - - - -
110A VAL* 2.9 35.9 + - + +
138A PHE* 5.1 0.9 - - - -
141A TYR* 3.3 16.3 + - - -
196A TYR* 3.2 12.6 + - - -
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.6 12.7 - - + +
103A TYR* 2.9 52.2 + - + +
104A ARG* 3.8 35.0 - - + +
105A PHE 3.2 0.2 - - - -
106A GLN* 1.3 76.8 - - - +
108A GLY* 1.3 57.5 + - - +
110A VAL* 3.9 2.3 - - - +
111A ARG* 2.9 45.7 + - - +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 3.8 4.9 + - - -
105A PHE 3.2 6.5 + - - -
107A MET* 1.3 76.0 - - - +
109A PHE* 1.3 66.5 + - - +
111A ARG* 3.2 26.8 + - - +
112A ASP* 3.0 27.5 + - - -
134A HIS* 4.0 6.7 - - - -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.7 16.6 - - - -
105A PHE* 3.0 19.0 + - + +
106A GLN* 3.6 16.8 - - - +
107A MET 3.3 0.2 - - - -
108A GLY* 1.3 74.0 - - - +
110A VAL* 1.3 65.7 + - - +
112A ASP* 3.0 6.4 + - - +
113A LEU* 2.9 34.9 + - + +
130A CYS* 4.0 24.9 - - + -
131A PHE* 3.7 37.7 - + - -
134A HIS* 3.2 33.2 + + + -
138A PHE* 4.0 21.8 - + - -
196A TYR* 3.7 21.5 - + - -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.8 46.7 - - + +
63A ARG* 5.2 7.2 - - + -
66A ILE* 4.1 25.8 - - + -
106A GLN* 2.9 24.7 + - + +
107A MET 4.1 0.7 - - - +
109A PHE* 1.3 74.7 - - + +
111A ARG* 1.3 58.9 + - - +
113A LEU* 3.2 9.2 + - + +
114A GLU* 2.9 44.3 + - + +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 5.5 0.8 + - - -
107A MET* 2.9 36.0 + - - +
108A GLY* 3.2 27.5 + - - +
109A PHE 3.1 0.2 - - - -
110A VAL* 1.3 78.7 - - - +
112A ASP* 1.3 66.1 + - - +
114A GLU* 3.2 7.0 + - - +
115A LYS* 3.0 48.0 + - + +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY 3.0 13.1 + - - +
109A PHE 3.7 6.5 - - - +
111A ARG* 1.3 77.9 + - - +
113A LEU* 1.3 63.1 + - - +
115A LYS* 3.1 33.0 + - - +
116A GLN* 3.0 25.5 + - + +
130A CYS* 3.8 14.4 - - - -
133A GLU* 3.7 13.2 - - - +
134A HIS* 3.1 31.6 + - + +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.7 9.9 - - + -
59A MET* 3.8 29.8 - - - +
62A GLU* 4.3 18.6 - - + -
109A PHE* 2.9 41.2 + - + +
110A VAL* 3.4 12.1 - - + +
111A ARG 3.2 0.2 - - - -
112A ASP* 1.3 76.9 - - - +
114A GLU* 1.3 58.2 + - - +
116A GLN* 2.9 18.4 + - - +
117A TYR* 3.1 9.5 + - - +
127A ILE* 4.0 27.6 - - + +
130A CYS* 3.6 27.8 - - + -
131A PHE* 5.1 4.0 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 3.5 20.9 - - + +
63A ARG* 2.7 43.6 + - - +
110A VAL* 2.9 30.6 + - + +
111A ARG* 3.6 7.0 - - - +
113A LEU* 1.3 75.3 - - - +
115A LYS* 1.3 62.2 + - - +
117A TYR* 3.3 20.3 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.0 38.2 + - - +
112A ASP* 3.1 33.7 + - - +
114A GLU* 1.3 78.4 - - - +
116A GLN* 1.3 66.5 + - - +
117A TYR 3.2 4.9 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP 3.0 14.4 + - - +
113A LEU* 2.9 11.1 + - - +
115A LYS* 1.3 83.5 - - + +
117A TYR* 1.3 62.5 + - - +
118A ASN* 3.5 2.6 + - - +
125A SER* 3.7 18.0 - - - -
126A GLU* 3.1 44.4 + - - +
127A ILE* 4.7 5.6 - - + -
129A PRO* 4.8 9.0 - - - +
130A CYS* 3.5 22.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il